Thermo Xcalibur

Library Browser
User Guide
Creating and Searching Spectral Libraries
Software Version 4.0
XCALI-97780 Revision A August 2015
© 2015 Thermo Fisher Scientific Inc. All rights reserved.

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Release history: Revision A, August 2015

Software version: Xcalibur 4.0 and later

For Research Use Only. Not for use in diagnostic procedures.

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Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Chapter 1 Overview of Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Library Browser Process Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
About Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Chapter 2 Exporting Spectrum Files to Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5

Opening a Raw Data File in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Viewing a Spectrum in Qual Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Subtracting Background Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Using the Subtract Background Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Subtracting Background Spectra Graphically. . . . . . . . . . . . . . . . . . . . . . . . . 14
Manually Exporting Spectrum Files from Qual Browser . . . . . . . . . . . . . . . . . . 16
Exporting Spectrum Files Automatically During Sequence Processing. . . . . . . . 16

Chapter 3 Managing Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Adding Spectrum Files to a User Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Managing the NIST Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Adding a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Deleting a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Copying a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Converting Libraries to Another Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Chapter 4 Searching Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31

Submitting a Spectrum to a Library Search in Qual Browser . . . . . . . . . . . . . . . 32
Setting Up and Running Automated Library Searches. . . . . . . . . . . . . . . . . . . . 37
Setting Up Library Searches in a Processing Method . . . . . . . . . . . . . . . . . . . 37
Setting Up the Qualitative Processing Sequence . . . . . . . . . . . . . . . . . . . . . . 55
Batch Reprocessing the Sequence and Printing Library Search Reports . . . . . 57

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Contents

Appendix A Library Sample Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61

Report from a Library Search During Batch Reprocessing . . . . . . . . . . . . . . . . . 62
Report from a Library Search Using Qual Browser . . . . . . . . . . . . . . . . . . . . . . 65

Appendix B Library Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67

Library Manager Application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Convert Libraries Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Manage Libraries Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Library Search Results Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75

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Preface
The Thermo Xcalibur™ mass spectrometry data system includes all the software needed to
create, search, and edit libraries. This guide describes the following:
• How to create and edit custom libraries for MS, MS/MS, or MSn spectra
• How to manage multiple libraries
• How to search multiple libraries

Contents
• Related Documentation
• Special Notices
• Contacting Us

Related Documentation
You can access the user guides (as PDF files) for the Xcalibur data system in two ways:
• From the computer taskbar by choosing Start > All Programs > Thermo Xcalibur >
Manuals > Xcalibur.
• From the home page – Roadmap view of the Xcalibur data system by choosing Help >
Manuals from the menu bar.

In addition to this guide, Thermo Fisher Scientific provides these guides for the Xcalibur data
system:
• Xcalibur Quick Start
• Xcalibur Getting Started Guide
• Xcalibur Data Acquisition and Processing User Guide
• Xcalibur Quan Browser User Guide
• Xcalibur Qual Browser User Guide
• XReport User Guide

Thermo Scientific Xcalibur Library Browser User Guide v

Preface

Help is available from within the Xcalibur data system and the National Institute of Science
and Technology (NIST) Mass Spectral Search application.

Special Notices
Make sure you follow the precautionary statements presented in this guide. The special
notices appear in boxes.

Special notices include the following:

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal
performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

vi Xcalibur Library Browser User Guide Thermo Scientific

 Preface

Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need. You
can use your smartphone to scan a QR code, which opens your email application or browser.

Contact us Customer Service and Sales Technical Support

(U.S.) 1 (800) 532-4752 (U.S.) 1 (800) 532-4752

(U.S.) 1 (561) 688-8731 (U.S.) 1 (561) 688-8736

us.customer-support.analyze us.techsupport.analyze
@thermofisher.com @thermofisher.com

 To find global contact information or customize your request

1. Go to www.thermoscientific.com.
2. Click Contact Us, select the Using/Servicing a Product option, and then
type the product name.
3. Use the phone number, email address, or online form.

 To find product support, knowledge bases, and resources

Go to www.thermoscientific.com/support.

 To find product information

Go to www.thermoscientific.com/lc-ms.
Note To provide feedback for this document:
• Send an email message to Technical Publications (techpubs-lcms@thermofisher.com).
• Complete a survey at www.surveymonkey.com/s/PQM6P62.

Thermo Scientific Xcalibur Library Browser User Guide vii

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Overview of Library Browser

This chapter gives a brief overview of the Library Browser window and a summary of the steps
for creating, editing, and searching custom libraries and printing the library search reports.

Contents
• Library Browser Process Overview
• About Library Browser

Use the Xcalibur Library Browser window to do the following:

• Create spectral libraries, including MS/MS fragmentation libraries.
• Run automatic or manual, post-acquisition library searches on MS/MS fragmentation
spectra.

Note Throughout this guide, the term Library Browser is used synonymously with the
term NIST MS Search (National Institute of Standards and Technology Mass Spectral
Search Program and Library System) to refer to the NIST™ MS Search desktop.

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1 Overview of Library Browser
Library Browser Process Overview

Library Browser Process Overview

Figure 1 provides a summary of the steps you perform to create, edit, and search libraries and
to print reports using the Xcalibur data system.

When using the Library Browser, you can export a spectrum from the Qual Browser window
to create a custom user library of MS/MS or MSn spectra, one entry at a time. To include a
spectrum in a library, open a raw data file1 in Qual Browser. Enhance a spectrum by averaging
several scans and by subtracting background scans. Then, export the spectrum to Library
Browser. See Exporting Spectrum Files to Library Browser for more information about this
process.

After exporting the spectrum to Library Browser, you can edit the spectrum information. For
example, you can change the name of the entry or specify the molecular weight or the CAS
(Chemical Abstract Service) registry number. You can even attach a chemical structure to the
library entry or select which mass-to-charge ratios to include. See Managing Libraries for
more information.

IMPORTANT For MS/MS and MSn spectra, however, do not delete any of the masses that
the data system detects because the presence of a particular mass-to-charge ratio, rather
than its intensity, is essential to identifying a compound.

Finally, the Xcalibur data system provides three ways to search libraries and print custom
reports:
• Automatically, by batch reprocessing data files in Sequence Setup with an appropriate
processing method (See Setting Up and Running Automated Library Searches for more
information.)
• Manually, by using a single spectrum in Qual Browser (See Submitting a Spectrum to a
Library Search in Qual Browser for more information.)
• Manually, by exporting a spectrum to Library Browser (See for more information.)

To print custom reports during sequence processing or batch reprocessing, you must select an
appropriate report template in the processing method. In addition, you can set up the
processing method to automatically export spectra to a user library in Library Browser during
sequence processing or batch reprocessing.

To print a custom report following a manual library search in the Qual Browser or Library
Browser window, choose File > Print from the Qual Browser menu bar or File > Print
Report from the Library Browser menu bar.

1 A raw data file is an unprocessed data file acquired from a Thermo Scientific instrument controlled by the
Xcalibur data system or equivalent application.

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 1 Overview of Library Browser
Library Browser Process Overview

Figure 1. Library Browser process overview

Create a Library Spectrum

Open a raw data file in Display a spectrum. Export the spectrum to

Qual Browser. Library Browser.

Create a Library or Add to an Existing Library

Specify the entry Name a new library or

Attach a structure Append other spectra
name, CAS#, and MW select an existing
(optional). to the library.
in Library Browser. library.

Search Libraries and Print Reports

Automatically, using RAW or RST files

Create a processing Add the processing method Set up batch processing to run a library
method with library to an existing sequence or search and print reports. Then, submit the
search parameters. a new sequence. sequence to the processing queue.

Manually, using a single spectrum

Specify library options; Print the report.

search.

Open a raw data file in

Qual Browser and
display the spectrum. Export a spectrum to Specify library options; Print reports.
Library Browser. search.

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1 Overview of Library Browser
About Library Browser

About Library Browser

The Xcalibur data system uses the NIST Mass Spectral Search Program and Library System.

Note Thermo Fisher Scientific provides the NIST Mass Spectral Search Program (version
2.0f ) with the Xcalibur data system.

The NIST libraries give access to the following:

• An extensive collection of chemical names
• Chemical Abstracts Service (CAS) registry numbers
• Molecular formulas and weights
• Chemical structures

You can create user libraries using spectra from the following sources:
• Exported from Qual Browser
• Exported automatically during sequence processing or batch reprocessing
• From other sources including text files

The program permits searches in many different ways:

• Find reference spectra that most closely match a submitted spectrum.
• Locate spectra or compounds that have certain specified characteristics (for example, the
abundance of certain peaks).
• Display the mass spectra of selected molecules.

For information about the features of the NIST Mass Spectral Search application, see the
Help system provided with the application.

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Exporting Spectrum Files to Library Browser

The Xcalibur data system includes a subset of the NIST mass spectral library called nistdemo.
The NIST/EPA/NIH Main Library contains more than 100 000 compounds with MS spectra
obtained primarily in the electron ionization (EI) scan mode.

The following procedures show how to export a spectrum file to the Library Browser window
using one of the steroid.raw data files in the following folder:
drive:\Xcalibur\examples\data

Follow these procedures to export spectrum files from Qual Browser to Library Browser or to
add spectrum files to an existing library during sequence processing or batch reprocessing.

Contents
• Opening a Raw Data File in Qual Browser
• Viewing a Spectrum in Qual Browser
• Subtracting Background Spectra
• Manually Exporting Spectrum Files from Qual Browser
• Exporting Spectrum Files Automatically During Sequence Processing

Opening a Raw Data File in Qual Browser

This procedure describes how to open a raw data file in the Qual Browser window. Open the
example raw data file, steroids14.raw, or a representative raw data file with a spectrum or
spectra of interest.

 To open a raw data file in the Qual Browser window

1. Open the Qual Browser window by doing one of the following:

• On the Xcalibur Roadmap view, click the Qual Browser icon, .
–or–
• On the Xcalibur Roadmap menu bar, choose GoTo > Qual Browser.

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2 Exporting Spectrum Files to Library Browser
Opening a Raw Data File in Qual Browser

2. Open a raw data file as follows:

a. Choose File > Open from the menu bar or click the Open icon, , in the toolbar.
The Open Raw File dialog box opens.
b. Browse to the location of the raw data file (Figure 2):
drive:\Xcalibur\examples\data
c. Select one of the steroids.raw files or a raw data file that you want to export a
spectrum from.
d. In the list at the bottom of the dialog box, select Default Layout.
The default layout provided with the Xcalibur data system displays a two-cell grid
with a chromatogram view and a spectrum view. The chromatogram view displays
the total ion chromatogram (TIC) and the spectrum view displays the spectrum from
the initial time point (RT = 0.0 minutes).
Figure 2. Open Raw File dialog box with the selection of steroid14.raw

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 2 Exporting Spectrum Files to Library Browser
Opening a Raw Data File in Qual Browser

e. Click Open.
The TIC chromatogram and the first mass spectrum for this data file appear in the
grid (Figure 3).
Figure 3. Default layout for a raw data file

Go to the next procedure, Viewing a Spectrum in Qual Browser.

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2 Exporting Spectrum Files to Library Browser
Viewing a Spectrum in Qual Browser

Viewing a Spectrum in Qual Browser

To view the mass spectrum of interest, use the interactive cells of the Qual Browser window.
The following procedure describes how to set up a four cell layout with the following views:
chromatogram, spectrum, scan filters, and averaged spectrum.

 To display the mass spectrum of interest

1. Beginning with the default layout of two cells in the grid, with the upper cell displaying a
chromatogram view and the lower cell displaying a spectrum view, add two more cells to
the grid:
• In the toolbar, click the Insert Cells Left icon, .
–or–
• On the menu bar, choose Grid > Insert Cells > Left.
All of the cells are inactive.
2. In the lower left cell, change the view to the scan filter view by right-clicking the cell and
choosing Scan Filters from the shortcut menu (Figure 4).

Note When none of the cells in the grid are pinned, clicking a cell makes it the active
cell. An active but unpinned cell has a gray border.

Figure 4. Choosing Scan Filters from the shortcut menu

Shortcut
menu

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 2 Exporting Spectrum Files to Library Browser
Viewing a Spectrum in Qual Browser

3. In the lower left cell, change the range of the scan filters view to the entire time range of
the chromatogram as follows:
a. Right-click the scan filter view and choose Ranges from the shortcut menu.
The Scan Filter Range dialog box opens.
b. If the value in the Time box is 0.00, type a dash and the end time point for the
chromatogram in the box (Figure 5). Otherwise, set the time range to the full time
range of the chromatogram (first time point–last time point).
Figure 5. Scan Filter Range dialog box with a time range specified in the Time box

c. Click OK.
The scan filters view lists all the scan filters in the raw data file (Figure 6).
Figure 6. Scan filters

4. In the upper left cell, change the TIC chromatogram to a mass range chromatogram for a
selected scan filter as follows:
a. Click the pin icon, , in the upper right corner of the cell (pin the cell) to make it
the active and pinned cell .
The last entry in the scan filter list is for a mass range chromatogram of all ions
between m/z 150 to 375.
b. Select the last entry in the scan filter list.
The last entry becomes surrounded with a box and the cursor becomes a page cursor.
c. Drag the page cursor to the upper left cell.
When you release the page cursor, the upper left cell displays the mass range
chromatogram for the selected scan filter (Figure 7).

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2 Exporting Spectrum Files to Library Browser
Viewing a Spectrum in Qual Browser

Figure 7. Mass range chromatogram for the selected scan filter (full MS2 m/z)

5. In the upper right cell, change the display to an averaged spectrum as follows:
a. Pin the cell.
b. Right-click the pinned cell and choose View > Spectrum from the shortcut menu.
c. In the upper left cell (full range MS2 chromatogram), drag the cursor across the
baseline width of the chromatographic peak.
An averaged spectrum appears in the upper right cell.
6. Pin the lower right cell and choose View > Chromatogram from the shortcut menu.
An unfiltered TIC chromatogram appears in the cell. Confirm that the grid looks similar
to the one in Figure 8.

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 2 Exporting Spectrum Files to Library Browser
Viewing a Spectrum in Qual Browser

Figure 8 shows the following views (clockwise from lower left): scan filter view, (filtered)
chromatogram view, (filtered) spectrum view (averaged, and chromatogram view
(unfiltered).
Figure 8. Qual Browser window
Chromatogram view (filtered) Spectrum view (averaged)

Scan filter view Chromatogram view (unfiltered)

Leave this layout open and go to the next procedure, Subtracting Background Spectra.

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2 Exporting Spectrum Files to Library Browser
Subtracting Background Spectra

Subtracting Background Spectra

You can subtract the background spectra in two ways: graphically by choosing Actions >
Subtract Spectra from the Qual Browser menu bar or automatically by specifying a
background file in the Subtract Background dialog box.

These procedures describe the two ways you can perform background subtraction:
• Using the Subtract Background Tool
• Subtracting Background Spectra Graphically

Using the Subtract Background Tool

Use the Subtract Background window to subtract a raw data file or a single scan from a raw
data file from any other selected raw data file. You can use this utility to subtract a background
spectrum from a raw data file or deconvolute merged or overlapping component peaks.

For more information, refer to the Xcalibur Qual Browser User Guide.

 To subtract the background from a raw data file

1. In the Qual Browser window, choose Tools > Background Subtract.

The Subtract Background window opens (Figure 9).
2. In the Input area, set up the data source information for the input file as follows:
a. In the File box, type the path name and file name of the input file, or click Browse
and locate the file with the Open dialog box.
b. In the Single Detector list, select the detector used to acquire the data of interest. If
the raw data file contains data from more than one detector, the All Detectors check
box is available. To subtract the background for all the data sources in the raw data
file, select the All Detectors check box.
c. In the Scan Filter list, select a scan filter from the list of scan filters that are stored in
the RAW file.
3. In the Background area, do the following:
a. To select the background file, type the path name and file name of the background
file in the File box or click Browse and locate the file using the Open dialog box.
b. Select the scope of the subtract background file operation as follows:
• To subtract the entire background file from the input file, select the Subtract
Whole File option.
• To subtract a single scan from the background file from each scan of the input
file, select the Subtract Single Scan (RT in Min) option and type the retention
time for the scan in the associated box.

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 2 Exporting Spectrum Files to Library Browser
Subtracting Background Spectra

c. Specify alignment and scaling as follows:

• To offset the subtraction of the background file from the input file, type the
required offset in the Alignment Offset (RT in Min) box.
• To scale the subtraction of the background file from the input file, type the
required factor in the Scaling Factor box.
4. In the Output area, specify the location of the output file by typing the full path location
in the Folder box, or by clicking Folder and browsing to the required location.
The Name box displays the output file as BG_<Input File> (Figure 9).
Figure 9. Subtract Background dialog box

5. Do one of the following:

• To abandon the file operation and close the dialog box, click Exit. The dialog box
closes.
• To start the subtract background file operation, click Proceed. When the background
subtraction is complete, a message box appears. Click OK to close the message box.
Click Exit to close the dialog box.

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2 Exporting Spectrum Files to Library Browser
Subtracting Background Spectra

Subtracting Background Spectra Graphically

To subtract background spectra, eliminating background peaks from either one range (either
side of the chromatogram peak of interest) or two ranges (both sides of the chromatogram
peak of interest), pin the spectrum view and use the cursor in the chromatogram view.

 To select two scan ranges for background subtraction

1. Pin the spectrum view to work interactively in the chromatogram view.

2. Right-click the spectrum view and choose Actions > Subtract Spectra > 2 Ranges from
the shortcut menu.
A crosshair cursor labeled –1 appears (Figure 10).
Figure 10. Crosshair cursor for background subtraction in the chromatogram view

3. In the chromatogram view, select a baseline region that is close to the chromatographic
peak of interest.
4. Drag the cursor away from the peak of interest and across a few scans that are
representative of the first scan range to subtract. Then, release the mouse button to define
the first range.
The cursor label changes to –2.
5. Select a baseline region on the other side of the peak of interest.
6. Drag the cursor away from the peak of interest and across a few scans that are
representative of the second scan range to subtract. Then, release the mouse button. to
define the second range.
When you release the mouse button, the data system subtracts an average of the selected
scans and redraws the spectrum view. The spectrum view header shows the number of
subtracted scans (Figure 11).

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 2 Exporting Spectrum Files to Library Browser
Subtracting Background Spectra

For example, SB: 49 0.12–0.54, 0.89–1.99 indicates the following:

• Qual Browser has applied background subtraction to the spectrum by using a 49-scan
average.
• Retention time ranges used in the subtraction are 0.12 to 0.54 min and 0.89 to
1.99 min.
Figure 11. Spectrum view after a 2-range background subtraction

 To undo background subtraction

Choose Actions > Subtract Spectra > Clear from the menu bar.

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2 Exporting Spectrum Files to Library Browser
Manually Exporting Spectrum Files from Qual Browser

Manually Exporting Spectrum Files from Qual Browser

To create a library entry for a custom library, you can export a spectrum to the Library
Browser window from either a spectrum view in the Qual Browser window or during
processing or batch reprocessing of raw data files in the Sequence Setup view.

Note For best results, read the documentation that the National Institute of Science and
Technology (NIST) provides with the NIST Mass Spectral Search application before you
export a spectrum file to the application.

This topic describes how to export a spectrum file from the Qual Browser window.

 To export a spectrum from Qual Browser to Library Browser

1. Open a raw data file in the Qual Browser window.

2. In the spectrum view, select the spectrum that you want to export (see Viewing a
Spectrum in Qual Browser).
3. Right-click the spectrum view and choose Library > Export to Library Browser.
The NIST Library Search window opens.
The data system converts the mass and intensity data of the spectrum to a text file and
copies the file to the Spec List pane. The Qual Browser window stays open. The data
system creates the following:
• A copy of the exported spectrum in the Xcalibur\Libspecs folder.
The file is given an (.msd) extension with the same file name as the original data file,
although this is truncated to eight characters (8.3 file name format).
• An index file containing details about all exported spectra.
The data system places the exported spectrum into the Spec List (Spectrum List). For
information about using the NIST Mass Spectral Search application, read the
documentation that is supplied with the application.

Exporting Spectrum Files Automatically During Sequence Processing

You can set up automatic exporting of spectra to a user library in a processing method. When
you run or batch reprocess a sequence that contains the processing method, you can turn on
the spectrum exporting feature.

When an exported spectrum file does not match any of the spectrum files in the selected
library, the data system appends the new spectrum file to the library.

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 2 Exporting Spectrum Files to Library Browser
Exporting Spectrum Files Automatically During Sequence Processing

 To set up a processing method that exports spectra to a user library

1. Choose GoTo > Processing Setup from the home page menu bar.
The Processing Setup window opens.
2. Choose View > Qual.
The Qual view of the Processing Setup window opens with the Identification page
displayed.
3. Click the Library Search Options tab to display the Library Search Options page.
4. Check the libraries that are in use as follows:
a. Click Search List.
The Search List dialog box opens.
b. Check the list of available libraries.
c. Add or remove libraries from the Available Libraries area, and then click OK to save
the changes and close the dialog box.
5. In the Append to User Library area, select the Enable check box.
Figure 12 shows the Append to User Library area on the Library Search Options page in
the Processing Setup – Qual view.
Figure 12. Append to user library area

6. In the User Library list, select an existing library or type the name of a spectral library
where you want to append the exported spectra.
If you type a new library name, the library is created only if a spectrum fails the matching
criteria. To ensure that spectrum files are appended to the specified library, enter the
highest possible values in the Thresholds boxes. The data system only appends spectrum
files that fail the matching criteria.

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2 Exporting Spectrum Files to Library Browser
Exporting Spectrum Files Automatically During Sequence Processing

7. Type threshold values for Match Factor, Reverse Match Factor, and Probability%. To
confirm that all spectra are appended to the library, type 999, 999, and 100 respectively.
During processing and after any requested enhancement of a relevant chromatogram peak
apex scan, the Xcalibur data system submits the spectrum to a library search:
• If the top hit from a library search exceeds (or is equal to) any one of the
threshold values, the data system returns the hit list and the spectrum is not
appended to the specified library.
• If the top hit fails to reach any of the threshold values, the data system discards
the hit list (no search results are reported) and appends the searched spectrum to
the specified library. Unless otherwise specified, the library is stored in the
NIST\MSSearch folder.
8. Save the processing method.

 To automatically export spectra to the designated library

1. From the Processing Setup window, open the Sequence Setup view by choosing GoTo >
Xcalibur Home Page from the menu bar. If the Sequence Setup view is not displayed,
open it by choosing View > Sequence Setup View.
2. Do one of the following:
• If you have not already acquired a set of raw data files, create a new sequence as
described in the Xcalibur Data Acquisition and Processing User Guide.
• If the acquisition sequence that contains the raw data files you want to process is not
open, choose File > Open. Then, in the Open dialog box, browse to the appropriate
folder, select the sequence file (SLD) of interest, and click Open.
3. If you have not already added the processing method to the sequence, do the following:
a. Double-click the Processing Method column.
The Select Processing Method dialog box opens (Figure 13).

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 2 Exporting Spectrum Files to Library Browser
Exporting Spectrum Files Automatically During Sequence Processing

Figure 13. Select Processing Method dialog box

b. Browse to the appropriate folder, select the processing method (PMD file) of interest,
and click Open.
4. Do one of the following:
• To export the spectra during data acquisition, in the Processing Actions area of the
Run Sequence dialog box, select the Qual check box.
• To export the spectra during batch reprocessing, in the Batch Reprocess dialog box,
select the Qual check box. Then, select the Peak Detection and Integration check
box and the Library Search check box.
If the library that is specified in the processing method does not exist, the Xcalibur data
system creates it.

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2 Exporting Spectrum Files to Library Browser
Exporting Spectrum Files Automatically During Sequence Processing

When a spectrum is added to a user library, it contains the following basic information:
• Complete mass/intensity list
• Name formatted as <filename>#<scannumber> RT: <rt> AV: <av> NL: <nl>, for
example: steroids02#1 RT: 0.01 AV: 1 NL: 2.14E3
• Comment showing the scan filter, such as T: + c Full ms2 363.30 [150.00 – 375.00]
• Molecular weight (Mol Weight) and CAS number set to zero

You might want to modify the basic information or provide the following:
• Chemical formula
• List of synonyms
• Molecular weight
• CAS number
• Chemical structure (in MOL, SDF, or MDL file format)
When you attach a structure to the file, you can automatically add the chemical formula
and molecular weight to the file by clicking From Structure as described in Managing the
NIST Libraries.

20 Xcalibur Library Browser User Guide Thermo Scientific

 3

Managing Libraries
In the Library Browser window, you can create, manage, and search user libraries. Use these
functions to create reference libraries from your own spectra.

Follow these procedures to add your spectrum files to a user library, to manage your library
list, and to convert your libraries to another format.
The data system stores the spectral libraries in the following folder:
drive:\Program Files\NISTMS\MSSEARCH\

Contents
• Adding Spectrum Files to a User Library
• Managing the NIST Libraries
• Converting Libraries to Another Format

Adding Spectrum Files to a User Library

You can add a spectrum file to a user library after you manually export the file from the Qual
Browser window. Or you can automatically add spectrum files to a user library during
sequence processing if you enable the Add to Library feature in the processing method and set
the appropriate match threshold criteria (see Exporting Spectrum Files Automatically During
Sequence Processing).

The following procedure describes how to add a spectrum that you manually exported from
the Qual Browser window to a user library.

 To add an unedited spectrum file to a library

1. Export a spectrum from Qual Browser. See Manually Exporting Spectrum Files from
Qual Browser.
The Library Browser window opens.
2. Choose Window > Librarian.
The Librarian window opens.

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3 Managing Libraries
Adding Spectrum Files to a User Library

3. In the Spec. List, select the spectrum that you want to add to a library (Figure 14).
The Spec List contains one row for each spectrum. The Src column lists the source of the
spectrum as one of the following: a text file (A), the Spectrum Editor (E), or a library.
User libraries are coded with the first two letters of the library name. The Name column
lists the spectrum name.
Figure 14. NIST MS Search 2.0 – Librarian window

Exported spectrum from the Text File label

peak at RT = 0.68 minutes in
the steroids05.raw data file

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 3 Managing Libraries
Adding Spectrum Files to a User Library

4. Click the Add to Library icon, , in the Librarian window toolbar.

The Choose Library to Copy To dialog box opens (Figure 15).
Figure 15. Choose Library to Copy To dialog box

5. Choose the library that you want to add the spectrum file to or type the name of a new
library in the box.
6. Click OK to add the new spectrum file to an existing library or to a new library.
A message box that lists the name of the library and the number of spectra in the library
appears (Figure 16).
Figure 16. Information about the library

7. Click OK to add the spectrum to the library.

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3 Managing Libraries
Managing the NIST Libraries

Managing the NIST Libraries

To add, delete, or move a library from the NIST libraries list, use the Manage Libraries page
of the Library Manager application. This section shows you how to complete the following
tasks:
• Adding a Library
• Deleting a Library
• Copying a Library

For more information about the Manage Libraries page of the Library Manager application,
see Library Manager Application.

 To open the Library Manager application

1. Open the Xcalibur home page – Roadmap view.

2. From the menu bar, choose Tools > Library Manager.
The Library Manager application opens with the Manage Libraries page
displayed (Figure 17).
Figure 17. Thermo Library Manager dialog box

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 3 Managing Libraries
Managing the NIST Libraries

Adding a Library
When you add a library to the NIST libraries list, either copy the library file to the local
computer or link to the library at a remote location without copying files.

 To add a library

1. Open the Manage Libraries page of the Library Manager application as described in
Managing the NIST Libraries.
2. Click Add.
The Add Library dialog box opens (Figure 18).
Figure 18. Add Library dialog box

3. In the Add Library dialog box, type the path for the new library file in the Source box or
click Browse to bring up the Browse for Folder dialog box and find the file of interest.
4. Select one of the two options:
• Copy the library to the local computer.
• Link to the library from either a remote location or computer.

Tip Because libraries can be large, you can often save time by selecting the Link
option rather than the Copy option.

5. Click OK.
The data system adds the selected library to the NIST Libraries list in the Library
Manager application.
6. If you have no more tasks to complete with the Library Manager, click Exit.

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3 Managing Libraries
Managing the NIST Libraries

Deleting a Library
 To delete a selected library in the NIST Libraries list

1. Open the Manage Libraries page of the Library Manager application as described in
Managing the NIST Libraries.
2. Select a library to delete from the NIST Libraries list.
3. Click Delete.
The system prompts you to confirm the deletion.
4. To delete the selected library, click Yes.
5. If you have no more tasks to complete with the Library Manager, click Exit.

Copying a Library
You can copy a selected library to another directory on the computer or network by using the
Archive feature.

 To copy a library

1. Open the Manage Libraries page of the Library Manager application as described in
Managing the NIST Libraries.
2. Select a library to copy from the NIST Libraries list.
3. Click Archive.
The Archive Library dialog box opens (see Figure 19).
Figure 19. Archive Library dialog box

4. Type the path for the copied library file in the Destination box or click Browse to bring
up the Browse for Folder dialog box and find the desired location.
5. To copy the selected library to the remote location, click OK.
6. If you have no more tasks to complete with the Library Manager, click Exit.

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 3 Managing Libraries
Converting Libraries to Another Format

Converting Libraries to Another Format

To convert all or any portion of a library to another format, use the Convert Libraries page of
the Library Manager application (Figure 20). Also, use this page to copy a library to another
location.

For more information about the Convert Libraries page, see Convert Libraries Page.
Figure 20. Convert libraries page

 To convert a library from one format to another

1. Open the Library Manager application as described in Managing the NIST Libraries.
2. Click the Convert Libraries tab to open the Convert Libraries page.
3. In the Source Library Details area, do the following:
• In the Type list, select the type of source library, based on the file name extension.
• In the Library box, type the path to the source library or click Browse to open the
Browse for Folder dialog box and find a file.

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3 Managing Libraries
Converting Libraries to Another Format

• In the Process Entries box, to convert only certain entries from the source library,
type the number range of the entries to convert. For example, to convert only entries
#100 to #200, type 100–200.
4. In the Target Library Details area, do the following:
• In the Type list, select the type of target library based on the file name extension.
• In the Library box, type the path to the target library or click Browse to open the
Browse for Folder dialog box and find a folder.

Note When you select NIST as the target library type, the default target library is
the library folder for the Xcalibur data system: C:\NIST02\MSSEARCH\.

When you select ICIS/GCQ/ITS 40 or MassLab as the target library type, the Title
box becomes available.
• In the Title box, type the title for the converted library.
5. In the Options area, do the following:
• Select either the Create/Replace option or the Append option.
Create/Replace is selected by default.
When you select NIST as the source library type, the Include Replicate Entries from
the NIST Library in the Target Library check box becomes available.
• Click the Include Replicate Entries from the NIST Library in the Target Library
check box to copy replicate entries.
When you select the Include Replicate Entries check box, the Replicate Library box
becomes available. The data system stores the default replicate library, REPLIB, in
the following folder:
drive:\NIST02\MSSEARCH\
• To use a different replicate library, type the path to the desired library in the Replicate
Library box or click Browse to open the Browse for Folder dialog box and find a
folder.
6. To begin the conversion process, click Convert.
The Conversion Status box displays sequential chronological (top to bottom) messages
such as:
Started the conversion on SEP 3, 1999 at 10:01, please wait
Finished the conversion on SEP 3, 1999 at 10:02
Converted 570 entries
7. If you have no more tasks to complete with the Library Manager, click Exit to close the
Library Manager application.

28 Xcalibur Library Browser User Guide Thermo Scientific

 4

Searching Libraries
After you create a custom library, you can use it for library searches. You can search spectral
libraries in three ways:
• Manually from within the Qual Browser window
• Manually from within the Library Browser window
• Automatically during sequence processing or batch reprocessing

Follow the procedures in this chapter to run library searches in the Qual Browser window or
during batch processing.

Contents
• Submitting a Spectrum to a Library Search in Qual Browser
• Setting Up and Running Automated Library Searches

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4 Searching Libraries
Submitting a Spectrum to a Library Search in Qual Browser

Submitting a Spectrum to a Library Search in Qual Browser

After you create a custom user library in the Library Browser window, you can submit a
spectrum to a library search from the Qual Browser window. Qual Browser uses the library or
libraries listed on the Search List page and the search parameters specified on the Search
Parameters page of the Search Properties dialog box.

 To submit a spectrum in Qual Browser to a library search

1. Open a raw data file in the Qual Browser window.

2. Open a chromatogram view as follows:
a. Click the pin icon, , in the upper right corner of the cell (pin the cell) where you
want to open the chromatogram view.
The pin icon changes to the pinned state, , to indicate that the chromatogram
view is the active and pinned cell.
b. Choose View > Chromatogram or click the View Chromatogram icon, , in the
toolbar.
3. Open a spectrum view as follows:
a. Click the pin icon, , in the upper right corner of the cell (pin the cell) where you
want to open the spectrum view.
The pin icon, , changes to the pinned state to indicate that the spectrum cell is
the active and pinned cell.
b. Choose View > Spectrum or click the View Spectrum icon, , in the toolbar.
4. To display or enhance a spectrum, choose from these options:
• With the spectrum cell pinned, click the chromatogram at the retention time of
interest (a peak apex, for example).
The spectrum from this time point appears in the spectrum view.
• To view a spectrum averaged across a peak, drag the cursor through the
chromatogram peak of interest.
• Enhance the spectrum, if necessary, by using background subtraction. For more
information on this step, see Subtracting Background Spectra.
5. Set up the library search options as follows:
a. Choose Actions > Library > Options.
The Search Properties dialog box opens with the Search List page displayed
(Figure 21).

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 4 Searching Libraries
Submitting a Spectrum to a Library Search in Qual Browser

Figure 21. Search Properties dialog box

b. Select the libraries that you want to search as follows:

• To move a library from the Available Libraries box to the Selected Libraries box,
select the library and click Add.
• To remove a library from the Selected Libraries box to the Available Libraries
box, select the library and click Remove.
• To change the search order of the selected libraries, select the library that you
want to move. Then, click the appropriate button:
– Click Top to move the library to the top of the list.
– Click Up to move the library Up by one position.
– Click Down to move the library down by one position.
– Click Bottom to move the library to the bottom of the list.
c. Click the Search Parameters tab.
The Search Parameters page opens (Figure 22).

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4 Searching Libraries
Submitting a Spectrum to a Library Search in Qual Browser

Figure 22. Search Parameters page

d. Make the appropriate selections and entries.

e. Click Apply to save the settings.
f. Click OK to close the dialog box.
6. To start the library search, do one of the following:
• Choose Actions > Library > Search from the menu bar.
• Click the Library Search Spectrum icon, , in the toolbar.
–or–
• Right-click the spectrum view and choose Library > Search from the shortcut menu.
Qual Browser displays the results of the library search in the Library Search Results
window (Figure 23).

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 4 Searching Libraries
Submitting a Spectrum to a Library Search in Qual Browser

Figure 23. Library Search Results window in Qual Browser

The interactive cells of the Library Search Results window show the following library
search results, displayed clockwise from the upper left quadrant:
• Hits list (a list of matching spectrum files)
• Molecular structure, including formula, molecular weight, name, and library index
number
• Difference spectrum (Raw Data minus Library Entry)
– Peaks above the x axis are relatively more intense in the spectrum than in the
library entry.
– Peaks below the x axis are relatively more intense in the library entry than in the
sample spectrum.
• Comparison of the sample spectrum and the library entry

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4 Searching Libraries
Submitting a Spectrum to a Library Search in Qual Browser

 To print the library search report

Note When you print a report from the Qual Browser window, the data system uses
the default printer for the data system computer.

1. Choose File > Print Preview.

The Print dialog box opens (Figure 24).
Figure 24. Print dialog box

2. Select the options for your print display.

3. To close the dialog box and preview the results, click OK.
4. To display the Print dialog box again, click Print and click OK.
5. To print the results, click OK in the second Print dialog box.
See Library Sample Reports for an example of library search results initiated from Qual
Browser.

For more information about this window, see Library Search Results Window.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

Setting Up and Running Automated Library Searches

You set up the parameters for a library search in a processing method. After you add the
processing method to a sequence, you can automatically process the data during a sequence
run or following data acquisition by batch reprocessing the sequence.

To run automated library searches and print reports, follow these procedures:
1. Setting Up Library Searches in a Processing Method
2. Setting Up the Qualitative Processing Sequence
3. Batch Reprocessing the Sequence and Printing Library Search Reports

Setting Up Library Searches in a Processing Method

To search libraries automatically, set up the qualitative parameters in the processing method.
You set up the qualitative parameters for a processing method in the Qual view of the
Processing Setup window.

Note Using the Library Search Constraints page requires specific knowledge about the
compounds you are looking for. When you are running a qualitative analysis on a sample
set, you might not know what compounds are in the samples, so it is not always possible
to use the parameters on the Library Search Constraints page to refine automated
processing.

 To open the Qual view of the Processing Setup window

1. Do one of the following:

• On the Xcalibur Roadmap view, click the Processing Setup icon, .
–or–
• On the Xcalibur home page menu bar, choose GoTo > Processing Setup.
2. On the Processing Setup menu bar, choose View > Qual.

Follow these procedures to set up the library search parameters for a processing method:
1. Setting Up the Identification Parameters for a Qualitative Processing Method
2. Setting Up the Library Search Options in a Processing Method
3. Specifying the Libraries for an Automated Search
4. Setting Up the Search Constraints for an Automated Library Search
5. Setting Up Reports for Automated Library Searches

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4 Searching Libraries
Setting Up and Running Automated Library Searches

Setting Up the Identification Parameters for a Qualitative Processing Method

Use the Identification page of the Processing Setup – Qual view to select the peak integration
algorithm and the scan filters.

 To set up the parameters on the Identification page of the Qual view

1. Open the Qual view of the Processing Setup window (see To open the Qual view of the
Processing Setup window).
2. Open a representative raw data file as follows:
a. From the menu bar, choose File > Open Raw File.
The Open Raw File dialog box opens.
b. Browse to and select an appropriate raw data file. Then, click Open.
The chromatogram and spectrum views become populated with data from the raw
data file (Figure 25).
Figure 25. Qual view of the Processing Setup window with an example raw data file

38 Xcalibur Library Browser User Guide Thermo Scientific

 4 Searching Libraries
Setting Up and Running Automated Library Searches

3. On the Identification page, do the following:

a. Select a detector type.
b. Select a peak detect algorithm in the Peak Detect list to specify how the data system
finds and processes chromatogram peaks.

ICIS This algorithm has been designed for MS data and has superior peak
detection efficiency at low MS signal levels. This is the Xcalibur
default peak detection algorithm.
Genesis This algorithm is the original Xcalibur peak detection algorithm and
has been provided for backward compatibility with Xcalibur 1.0 data
system studies.
Avalon This algorithm supports detectors other than MS and detects negative
chromatographic peaks and shoulders more accurately than Genesis or
ICIS.

c. In the Filter list, select a scan filter.

d. To accept current changes to the Identification page, click OK.

e. To set advanced parameters, click Advanced (Figure 26).

Note For the following procedure, the ICIS Advanced Parameters dialog box
opens. If you choose another peak detection algorithm, a different Advanced
Parameters dialog box opens. Fill in the values that are appropriate for the
method.

f. Confirm that the INCOS Noise option is selected in the Noise Method area.
Figure 26. ICIS Advanced Parameters dialog box

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4 Searching Libraries
Setting Up and Running Automated Library Searches

g. To close the dialog box and return to the Processing Setup window, click OK.
h. To apply changes to the Identification page, click OK.

Go to the next procedure, Setting Up the Library Search Options in a Processing Method, to
set up the library search options.

Setting Up the Library Search Options in a Processing Method

Use the Library Search Options page (see Figure 27) in the Qual view of the Processing Setup
window to set up the library search options in a processing method.

For more information about creating a processing method, refer to the Xcalibur Data
Processing and Acquisition User Guide.

Note The Xcalibur data system uses the NIST Mass Spectral Search Program algorithms
to perform its library searches. The algorithms and related software are distributed by the
Standard Reference Data Program of the National Institute of Standards and Technology
and are the copyright of the US Secretary of Commerce.

 To set up the library search option parameters for a processing method

1. Set up the identification parameters as described in Setting Up the Identification

Parameters for a Qualitative Processing Method, if you have not already done so.
2. Click the Library Search Options tab to open the Library Search Options page
(Figure 27).
Figure 27. Library Search Options page in the Qual view of the Processing Setup window

40 Xcalibur Library Browser User Guide Thermo Scientific

 4 Searching Libraries
Setting Up and Running Automated Library Searches

3. In the Search Type area, do one of the following:

• To submit processed spectra to an identity search, select the Identity option. Then,
select one of the three Identity search types:
– Select the Normal option to use a normal identity search.
– Select the Quick option to use a quick identity search.
– Select the Penalize Rare Compounds option if you want a modified normal
identity search.
• To submit processed spectra to a similarity search, select the Similarity option. Then
select one of the three Similarity search types:
– Select the Simple option to use a Simple Similarity search.
– Select the Hybrid option to use a Hybrid Similarity search.
– Select the Neutral Loss option if you want a Neutral Loss Similarity search.
The difference between the two search types is primarily in the weightings of the
spectrum as a function of mass.
4. In the Options area, do the following:
• To limit the number of search results to be returned by a library search and reported
in the result file, type a number in the Maximum Number of Hits box.
• If you know the molecular weight of your target analyte and want to restrict the
search to library compounds of the same molecular weight, select the Search with
MW = check box and type the molecular weight in the associated box.
When you select the Search with MW= option, the Molecular Weight option on the
Library Search Constraints page becomes unavailable.
• To select the sorting method for hits, do one of the following:
– To sort hits by Reverse Match Factor, select the Reverse Search check box.
– To sort hits by the Forward Match Factor, clear the Reverse Search check box.
5. To include mass defect values for library searches, select the Enable check box in the Mass
Defect area.
6. To add new spectra to a user library, do the following:
a. In the Append to User Library area, select the Enable check box.
The User Library list and the parameters in the Thresholds area become available.

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4 Searching Libraries
Setting Up and Running Automated Library Searches

b. Select the user library and specify the spectrum thresholds as follows:
• From the User Library list, select the target user library.
• Type a threshold value in the Match Factor box.
• Type a threshold value in the Reverse Match Factor box.
• Type a threshold value in the Probability (%) box.
7. To save the settings on the Library Search Options page, click OK.

Leave the Library Search Options page open and go to the next procedure, Specifying the
Libraries for an Automated Search.

Specifying the Libraries for an Automated Search

When you set up a processing method to automate library searches, you must specify the
libraries to be searched.

 To specify the libraries to be searched

1. On the Library Search Options page of the Processing Setup – Qual view, click Search
List (Figure 27 on page 40).
The Search List dialog box opens (Figure 28).
Figure 28. Search List dialog box

2. To select a library to search, select the library name in the Available Libraries list and click
Add to move it to the Selected Libraries list.
3. Click OK to select that library and return to the Processing Setup – Qual view.

To set up search constraints for the automated library search, go to the next procedure, Setting
Up the Search Constraints for an Automated Library Search. Otherwise, go to Setting Up
Reports for Automated Library Searches to add a library search report to the method.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

Setting Up the Search Constraints for an Automated Library Search

For processing efficiency, constrain an automated library search using some of the options on
the Library Search Constraints page of the Processing Setup – Qual view (these are all
normally not active). For example, you can exclude certain high intensity ions that appear in
many compounds or that are present in the spectrum background. You can target a search to a
particular range of molecular weights or to compounds containing certain elements.

Setting up the options on the Library Search Constraints page requires specific knowledge
about the target compounds in the chromatogram. Acquiring this knowledge is not always
possible with a qualitative analysis.

The Library Search Constraints page contains five groups of options to constrain the library
search (Figure 29). To display the Library Search Constraints page, from the Qual view of the
Processing Setup window, click the Library Search Constraints tab.

See the following topics to set up the constraints:

• Applying a Molecular Weight Constraint
• Applying the Other Databases Constraint
• Applying a Name Fragment Constraint
• Applying Element Constraints
• Applying Mass Spectral Peak Constraints

Figure 29. Library Search Constraints page from Qual View

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4 Searching Libraries
Setting Up and Running Automated Library Searches

Set parameters and save your settings by clicking OK. To save your settings for future
searches, click Save as Default.

Applying a Molecular Weight Constraint

Follow this procedure to set up the parameters in the Molecular Weight area of the Processing
Setup – Qual view.

 To limit the library search to compounds with a specific molecular weight or

molecular weight range
1. Select the Enable check box in the Molecular Weight area (Figure 30).
Figure 30. Molecular weight area

2. In the Range box, type a molecular weight or molecular weight range.

To specify a range, use the format low mass–high mass. The valid range is 1 to 999 999. All
search results must satisfy the specified molecular weight range.

Note This constraint is not available if you have already selected the Search with
MW= check box on the Library Search Options page of the Processing Setup – Qual
view.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

Applying the Other Databases Constraint

Follow this procedure to set up the parameters in the Other Databases area of the Processing
Setup – Qual view.

 To limit the library search to entries in the NIST library that are also featured in other
databases
1. Select the Enable check box in the Other Databases area (Figure 31). NIST library entries
contain references to other commercial databases if they contain information about the
compound.
Figure 31. Other databases area

2. Select one or more databases from the available list. To use a database constraint, select its
check box. If you do not want to use a database constraint, make sure its check box is
clear.

Fine Commercially Available Fine Chemical Index

TSCA Toxic Substances Control Act Inventory
RTECS Registry of Toxic Effects of Chemical Substances
EPA EPA Environmental Monitoring Methods Index
USP US Pharmacopoeia/U.S.A.N.
HODOC CRC Handbook of Data of Organic Compounds
NIH NIH-NCI Inventory File
EINECS European Index of Commercial Chemical Substances
IR NIST/EPA Gas Phase IR Database

The data system only reports search results if they feature in one or more, but not
necessarily all, of the selected databases.

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4 Searching Libraries
Setting Up and Running Automated Library Searches

Applying a Name Fragment Constraint

Follow this procedure to set up the parameters in the Name Fragment area of the Processing
Setup – Qual view.

 To limit the search to compounds with a specific name or name fragment

1. Select the Enable check box in the Name Fragment area (Figure 32).
The Name box accepts a text string (up to 39 characters) to represent a fragment of a
compound name, for example, “cyclo”. The library search filters the search results and
only returns those containing the specified text in their names. The entry is not case
sensitive; for example “CYCLO” returns compounds containing the fragments “cyclo”,
“Cyclo”, “CYCLO”, and any other case permutations.
Figure 32. Name fragment area

2. Type a name fragment in the Name box.

Applying Element Constraints

Follow this procedure to set up the parameters in the Element Constraints area on the Library
Search Constraints page of the Processing Setup – Qual view.

To constrain the library search to compounds with specific element profiles, follow one of
these methods:
• To use the Individual Elements constraints
• To use the Elements in Compound constraints

 To use the Individual Elements constraints

1. In the Elements Constraints area, select the Enable check box.

Use the Individual Element area to set specific criteria about the elements required in a
library search result (hit). For example, the entries shown in Figure 33 would only return
search results for compounds that contain more than five fluorine atoms and exactly three
chlorine atoms.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

Figure 33. Element Constraints area

You do not need to provide a complete elemental profile. The library search returns
compounds if they satisfy all the specified criteria regardless of any other elements
present. Use this option to specify which elements you do not want to be in a library hit
(spectrum match). For example, C = 0 confirms that no search results contain carbon.
When a contradiction occurs, for example, C < 2, and C > 4, the data system displays an
error message. Correct the contradiction to proceed.
2. In the Individual Element area, do the following for each element that you want to
constrain:
• In the Element column, type the required element abbreviation. You must use the
IUPAC approved abbreviation for each element. For example, type capital F for
fluorine or Cl for chlorine.
• In the Condition column of the same row, select from the three available conditions:
< (less than), > (greater than), or = (equal to).
• In the Value column of the same row, type the required number of atoms for the
element constraint condition.

 To use the Elements in Compound constraints

1. In the Elements Constraints area, select the Enable check box.

2. In the Elements in Compound area, in the Elements box, type the IUPAC approved
abbreviation for each element (see Figure 33) that must be present in returned search
results. Separate each element in the list (of up to 30 characters) by the character specified
as the list separator character. Refer to “Changing the List Separator Character” in the
Xcalibur Data Acquisition and Processing User Guide for more information.
3. Select the All option to have the returned search results contain all, and only, the listed
elements. For example “C, H, O” would return HCHO but not CO2, CH4, or CH2Cl2.

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4 Searching Libraries
Setting Up and Running Automated Library Searches

4. Select the Some option to have the returned search results contain at least one of the
specified elements and no elements other than those listed. For example “C, H, O” would
return CO2, CH4, and HCHO but not CH2Cl2 (Cl not allowed).
If you leave the box blank, the data system does not apply the Elements in compound
constraint function. If you type an invalid element, the data system reports an error when
you click anywhere else on the page.

If there are no contradictions, you can use the two types of elemental constraints together. For
example, if the Individual Element area contains “C=0” or “C<1" and the Elements In
Compound box contains “C” when the All option has been selected, the data system displays
an error message. Correct the contradiction to proceed.

Applying Mass Spectral Peak Constraints

Follow this procedure to set up the parameters in the Mass Spectral Peak Constraints area of
the Processing Setup – Qual view.

The Mass spectral peak constraint feature builds a profile of ions and their abundances to be
matched against library entries during the search.

For information about the parameters in the Mass Spectral Peak Constraints area, refer to the
Xcalibur Data Acquisition and Processing User Guide.

 To apply and set up mass spectral peak constraints

1. Select the Enable check box in the Mass Spectral Peak Constraints area (Figure 34).
The search algorithm only returns search results matching the specified constraints.
Figure 34. Example of a relative mass spectral peak constraint

2. Select the Absolute or Relative option:

• To evaluate all table entries as a percentage of the base (largest) ion in the spectrum,
select the Absolute option.
• To treat the first entry as an absolute Normal or Loss type, select the Relative option.
The data system considers subsequent entries in the table relative to the first.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

3. For each mass spectral peak that you want to constrain, do the following in the Mass
Spectral Peak Constraints table:
• In the Type list, do the following:
– Select from the four available types for the Absolute option: Normal, Loss, Rank
or Maxmass.
– Select from the two available types for the Relative option: Normal or Loss.
• In the m/z column of the same row, do the following:
– For a Normal, Rank, or Maxmass type constraint, type the m/z value of the mass
spectral peak to be constrained. The valid range is 0–2000,
– For a Loss type constraint, type the value of a neutral loss. The valid range is
0–64.
• In the From column of the same row, do the following:
– For a Normal, Loss, or Maxmass type constraint, type the minimum abundance
of the constrained mass spectral peak.
– For a Rank type constraint, type the lowest position of the ion in an intensity
ordered list of spectral peaks.
For the Rank type constraint, the From value cannot be greater than the To
value. If the From value equals the To value, the designated ion must have that
rank in the retrieved spectrum.
• In the To column of the same row, do the following:
– For a Normal, Loss, or Maxmass type constraint, type the maximum abundance
of the constrained mass spectral peak.
– For a Rank type constraint, type the highest position of the ion in an intensity
ordered list of spectral peaks.

Note If you switch between Absolute and Relative modes, the Xcalibur data
system prompts you with a warning message before clearing all rows in the grid.

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4 Searching Libraries
Setting Up and Running Automated Library Searches

Setting Up Reports for Automated Library Searches

To produce and print reports automatically, specify report options from the Reports view of
the Processing Setup window after setting up the library search parameters.

 To display the data in the format of a custom report template

1. In the Processing Setup window, choose View > Reports.

The Reports view opens (see Figure 35).
Figure 35. Reports view of the Processing Setup window

2. If the Apply Changes? dialog box opens, read the message and click Yes.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

3. Click the Enable cell in the Sample Reports area. When a check box appears, select the
check box to make row 1 active (Figure 36).
Figure 36. Reports view with Row 1 active

4. Specify the sample types in row 1 as follows:

a. To exclude the standards from the report, click Yes in the Std column and clear the
check box.
b. To exclude the quality control samples, click Yes in the QC column and clear the
check box.
c. Click Yes in the Other column and clear the check box.

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4 Searching Libraries
Setting Up and Running Automated Library Searches

5. Select a report template in row 1 as follows:

a. Double-click the Report Template Name column.
The Browse for Sample Report Template dialog box opens.
b. Select the LibrarySearchReport.xrt template or your own custom template for
library reports. Then, click Open.
6. To apply changes to the Reports view, click OK.
Figure 37 shows the Reports view and a specified Report Template Name.
Figure 37. Reports view of the Processing Setup window

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

7. Save the processing method as follows:

a. Choose File > Save As.
The File Summary Information dialog box opens (Figure 38).
Figure 38. File Summary Information dialog box

b. Type file summary information in the Description box and click OK.
The Save As dialog box opens.

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4 Searching Libraries
Setting Up and Running Automated Library Searches

c. Type a name for the processing method in the File Name box (Figure 39).
Figure 39. Save As dialog box

d. To save the method and return to the Reports view, click Save.
8. To close the Processing Setup window and return to the Xcalibur home page, choose File
> Exit.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

Setting Up the Qualitative Processing Sequence

To search libraries and print reports automatically, set up a processing sequence that contains
the raw data files to be processed and the processing method with the library search
parameters.

For information about creating a processing method for automated library searches, see
Setting Up Library Searches in a Processing Method.

 To set up the processing sequence

1. Open the Sequence Setup view by doing one of the following:

• On the home page – Roadmap view, click the Sequence Setup icon, .
–or–
• On the Xcalibur home page, choose View > Sequence Setup View
from the menu bar.
2. From the menu bar, choose File > Open.
The Open dialog box opens.
3. Select the sequence file (SLD) that contains the raw data files that you want to reprocess.
Then, click Open.
The sample list appears in the Sequence Setup view (Figure 40).
Figure 40. Sequence Setup view

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4 Searching Libraries
Setting Up and Running Automated Library Searches

4. Modify the sample list as appropriate:

• To exclude samples from the list, select rows to exclude and choose Edit > Delete
Row. The data system displays a message box to confirm the Delete Row command.
Click Yes.
• To view the Sample Type column, click the left side of the horizontal scroll bar at the
bottom of the workspace. Double-click the Row 1 cell in the Sample Type column to
display a drop-down list. Then, scroll up to select Unknown.
• Expand the width of the Path column to confirm that the directory is the one storing
the raw data files. For example, raw data files containing steroids data are found in
C:\Xcalibur\examples\data.
5. To select the processing method of interest, do the following:
a. Double-click in row 1 of the Processing Method column.
The Select Processing Method dialog box opens.
b. Select the processing method that you want to use to run an automated library
search. Then, click Open.
The data system populates the Processing Method column with the selected
processing method.
6. To save the sequence list file, choose File > Save As.
The File Summary Information dialog box opens.
7. Type a description in the Comment box and click OK.
The Save As dialog box opens.
8. Type a name in the File Name box to name the sequence.
9. Click Save to save the sequence list and return to the Sequence Setup view.

To batch reprocess the sequence and print reports, go to the next procedure, Batch
Reprocessing the Sequence and Printing Library Search Reports.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

Batch Reprocessing the Sequence and Printing Library Search Reports

Follow this procedure to batch reprocess a sequence and print reports.

Tip During batch reprocessing, the data system sends the user-specified reports to the
default printer for the data system computer. You can select the paper size and page
orientation in the Page Setup dialog box. To open this dialog box, choose File > Page
Setup from the menu bar.

 To batch reprocess a sequence and print library search reports

1. Set up the processing sequence as described in Setting Up the Qualitative Processing

Sequence.
2. If you closed the processing sequence, open it in the Sequence Setup view by choosing
File > Open from the menu bar.
3. To select the rows in the current sequence to process, select the row number in the first
row to process and drag the cursor to the bottom row.
The data system highlights the selected rows.
4. Do one of the following:
• Click the Batch Reprocess icon, , in the toolbar.
–or–
• Choose Actions > Batch Reprocess.
The Batch Reprocess Setup dialog box opens (Figure 41).

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4 Searching Libraries
Setting Up and Running Automated Library Searches

Figure 41. Batch Reprocess Setup dialog box

5. Confirm that the Process Rows box lists all row numbers (for example 1–2). If the
numbers are missing, double-click the box and type the row numbers.
6. To perform a library search, select the Qual check box. Then, select the Peak Detection
& Integration check box, the (optional) Spectrum Enhancement check box, and the
Library Search check box.
7. To print the library search sample report, select the Reports check box. Then, select the
Print Sample Reports check box.
8. To initiate batch processing of the selected samples, click OK. If the data system prompts
you to save your changes, click Yes in the confirmation box.

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 4 Searching Libraries
Setting Up and Running Automated Library Searches

9. To display the Processing Status window (Figure 42), click the Queue Manager task in
your computer task bar.
Figure 42. Processing Status window

Two beeps signal the end of batch processing.

10. Check your printed reports to see that they provide the information you wanted.

Thermo Scientific Xcalibur Library Browser User Guide 59

 A

Library Sample Reports

This appendix contains samples of possible library search reports printed during batch
reprocessing of a sequence or from within the Qual Browser window.

Contents
• Report from a Library Search During Batch Reprocessing
• Report from a Library Search Using Qual Browser

Thermo Scientific Xcalibur Library Browser User Guide 61

A Library Sample Reports
Report from a Library Search During Batch Reprocessing

Report from a Library Search During Batch Reprocessing

The Xcalibur data system prints library search reports automatically when you process or
batch reprocess a sequence. This library search report was generated with the
LibrarySearchReport.xrt template. For more information, see Setting Up and Running
Automated Library Searches.

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 A Library Sample Reports
Report from a Library Search During Batch Reprocessing

Thermo Scientific Xcalibur Library Browser User Guide 63

A Library Sample Reports
Report from a Library Search During Batch Reprocessing

64 Xcalibur Library Browser User Guide Thermo Scientific

 A Library Sample Reports
Report from a Library Search Using Qual Browser

Report from a Library Search Using Qual Browser

The following is an example of a library search report that you can print from the Qual
Browser window. For more information, see Submitting a Spectrum to a Library Search in
Qual Browser.

Thermo Scientific Xcalibur Library Browser User Guide 65

 B

Library Browser
This chapter describes the Library Manager application that you can access from the Tools
menu on the Xcalibur home page and the Library Search Results window that opens when
you submit a library search from the spectrum view of the Qual Browser application.

Contents
• Library Manager Application
• Library Search Results Window

For more information about the NIST MS Search application, refer to the Help provided
with the application.

Library Manager Application

Use the Library Manager application to manage NIST libraries used with the NIST search
software and to convert libraries between the ICIS/GCQ/ITS 40, MassLab, NIST, and
ANDI-MS formats.

Xcalibur Library Manager supports the following conversions.

To ICIS/GCQ/ITS 40 MassLab ANDI-MS NIST

From

ICIS/GCQ/ITS 40   
MassLab   
ANDI-MS   
NIST   

Note The Xcalibur data system does not directly support INCOS, LAB-BASE, or
JCAMP library conversions. However, MassLab data system users have a conversion
program to convert from a LAB-BASE user library to a MassLab user library. In addition,
a conversion tool exists in ICIS (a UNIX system) that can convert a LAB-BASE user
library to a MassLab user library.

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B Library Browser
Library Manager Application

The Library Manager application has the following pages:

• Convert Libraries Page
• Manage Libraries Page

Convert Libraries Page

Use the Library Manager – Convert Libraries page to convert one type of source library to
another type of library at a target location and to copy a library to another location. This table
describes the parameters on the Convert Libraries page.

Table 1. Convert Libraries page parameters (Sheet 1 of 3)

Parameter Description
Source Library Details
Type [Source] Specifies the source library file type that you want to convert to
another file type.

Type or select any of the following file types: ICIS/GCQ/ITS 40

(LIB or LBR), MassLab (IDB), ANDI-MS (CDF), NIST, or
AutoMass (SPR, PRS, NAM, or HDR).
Library/Browse Specifies the source library that you want to convert. To change
[Source] the library, click Browse and select the path to the source library
on your computer or network.
Process Entries Specifies the number range of the library entries that you want to
[Source] convert from the source library. If you leave the box empty, the
Xcalibur data system converts all entries. The format is First
Entry–Last Entry. For example, to convert library entry #100
through library entry #200, type 100–200 in the Process Entries
box.
Target library details
Type [Target] Specifies the target library file type when converting the source
library.

If you select source library file type ICIS/GCQ/ITS 40, MassLab,

ANDI-MS, or NIST, you can select from the following target
library file types: ICIS/GCQ/ITS 40 [(LIB) or (LBR)], MassLab
(IDB), NIST, or ANDI-MS (CDF).

If you select source library file type AutoMass, you can only select
the NIST target library file type.

If you select the library type NIST, the Xcalibur data system
displays the path to the NIST library folder in the Library box.
You specified this location when you installed NIST.

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 B Library Browser
Library Manager Application

Table 1. Convert Libraries page parameters (Sheet 2 of 3)

Parameter Description
Library/Browse Specifies the file folder to store the converted library file. To
[Target] change the folder, click Browse and select the target folder on
your computer or network.
Title [Target] Type in a title for the ICIS/GCQ/ITS 40 library or for the Mass
Lab library that you create during the conversion. You can add a
title to the new library using any format.
Note This box in the Target library details area only becomes
active when you select an ICIS/GCQ/ITS 40 or MassLab
library.
Add the library to the Selecting this check box adds the converted library to the NIST
NIST software for use software for use with the data system.
with Xcalibur
Options
Target library action: Select this option to create a new library in the target directory or
Create/Replace to replace an existing library. You can also append (add) the new
(converted) entries to a previously created target library.
Target library action: Select this option to append (adds) the new (converted) entries to
Append a previously created target library. You can also create a new library
in the target directory or to replace an existing library.
Include replicate Selecting this check box includes replicate entries in the target
entries from the NIST library.
library in the target
Note This check box is only available if you are converting from
library
a NIST library to another format.
Replicate Specifies the location of a replicate library. To change the replicate
library/browse library, click Browse and select the folder for the replicate library
on your computer or network. If you specify a replicate library, the
Xcalibur data system adds replicate entries into the appropriate
replicate library.

If you select the library type NIST, the Xcalibur data system
displays the path to the NIST replicate library folder in the
Library box. You specify this location when you install NIST
software.

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B Library Browser
Library Manager Application

Table 1. Convert Libraries page parameters (Sheet 3 of 3)

Parameter Description
Button
Convert Starts the library conversion you have specified using the Convert
Libraries page. The data system opens the Library Conversion
Status dialog box and displays the Conversion Status progress bar
and the Conversion Status box. The Status bar displays messages
such as the following:
Processed 100% of the entries, continuing on

The Conversion Status box displays sequential chronological (top

to bottom) messages such as the following:
• Started the conversion on SEP 3, 1999 at 10:01, please wait
• Finished the conversion on SEP 3, 1999 at 10:02
• Converted 570 entries

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 B Library Browser
Library Manager Application

Manage Libraries Page

Use the Library Manager – Manage Libraries page to add a library to the NIST libraries list or
to delete a library from the NIST libraries list. You can also copy a library to another location.
This table describes the parameters on the Manage Libraries page.
Table 2. Manage Libraries page parameters (Sheet 1 of 2)
Parameter Description
NIST Libraries
NIST Libraries list Lists all of the NIST libraries currently available on your
computer or network. You can add libraries to this list, delete
libraries from this list, and copy libraries on the list to another
location.
Buttons
Add Adds a library to the NIST Libraries list. The Add Library dialog
box opens.

The Add Library dialog box has the following parameters:

• Source: Specifies the name and location of the library that you
want to add.
• Action options:.
– Copy the library to the local computer: Select this option
to copy the selected library to your computer.
– Link to the library from either a remote location or
computer: Select this option to access the library
remotely.

Because libraries can be large, you might save time by using the
Link option rather than the Copy option.

Click OK when you have selected the library you want to add and
selected Action options.

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B Library Browser
Library Manager Application

Table 2. Manage Libraries page parameters (Sheet 2 of 2)

Parameter Description
Delete Deletes the library that you have previously selected in the NIST
Libraries list. Select the library that you want to delete from the
NIST Libraries list. Click Delete. The Delete Library message box
opens with the following message:
Are you sure you want to delete the selected NIST library?

Click Yes. The Xcalibur data system removes the library from the
list.
Archive Copies a selected library to another directory on your computer or
network. Select the library that you want to copy to another
directory. Click Archive. The Archive Library dialog box opens.

The Archive Library dialog box has the following parameters:

• Parameter
• Description
• Destination: Specify the location for the selected library.

Use Browse to select a destination for the selected file. Click OK.
The data system makes a copy of the selected NIST library and
stores it in the selected directory.

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 B Library Browser
Library Search Results Window

Library Search Results Window

Qual Browser displays this window in its workspace when you submit a spectrum in a
spectrum view to a library search or when you open a result file containing library search
results from qualitative processing.

The Library Search Results window displays matching library spectra (hits) in a four-pane
arrangement. Clockwise from the top left, the four panes are Hit List, Molecular Structure,
Difference Spectrum, and Comparison.

Hit List
The Hit List lists the best matches found during the library search. Three factors describe the
accuracy of the match to your spectrum:

SI A direct matching factor for the unknown and the library spectrum.
RSI A reverse search matching factor ignoring any peaks in the unknown that are
not in the library spectrum.
Prob A probability factor based on the differences between adjacent hits in an SI
ordered list.

With the SI and RSI matching factors, a perfect match results in a value of 1000. As a general
guide 900 or greater is an excellent match; 800–900, a good match; and 700–800, a fair
match. A matching factor less than 600 is a poor match. Unknown spectra with many peaks
tend to yield lower match factors than otherwise similar spectra with fewer peaks.

The probability factor is a complex parameter based on the SI matching factor and the
difference between adjacent matches. If a hit has an SI match factor > 900 and the next best
hit has a match factor of 300, the probability of the compound being correctly identified is
high. Conversely, if several hits are returned with very similar SI matching factors, the
probability of a correct assignment is low.

Molecular Structure
Shows the formula, structure, molecular weight, name and library index number of the
currently selected hit in the Hit List.

Difference Spectrum
Compares the submitted spectrum with the currently selected library spectrum in the Hit
List. Peaks above the x axis are relatively more intense in the sample than the library entry.
Negative peaks are relatively more intense in the library entry than in the sample spectrum.

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B Library Browser
Library Search Results Window

Comparison
Displays the submitted spectrum above the currently selected library spectrum in the Hit List
pane (list of matching spectrum files).

Note Avoid making positive assignments based solely on the statistical result of a library
search. The Xcalibur data system might identify a compound with an unusual structure
(or, more importantly, an unusual mass spectrum) in a definitive way. More usually, your
unknown might be a member of a class of compounds with very similar mass spectra. The
ability of Qual Browser or any search system to distinguish between them is limited. In
many cases, the best that the search algorithm can do is identify a class of compounds that
have similar mass spectra — and usually similar structure. In most cases, you should seek
confirmation by other analysis techniques.

74 Xcalibur Library Browser User Guide Thermo Scientific

 I

Index

A EPA Environmental Monitoring Methods Index database 45

European Index of Commercial Chemical Substances
Actions menu 14
database 45
adding
libraries to the NIST libraries list 25
spectrum files to a user library during sequence F
processing 16 file types, library 68
spectrum files to a user library manually 21 Fine Chemical Index database 45
ANDI-MS user library 67
Append to User Library area 17
G
grid layout, Qual Browser 8
B
background subtraction 14
batch processing
H
adding spectra to a library during 19 Hit list, description 73
running library searches during 37 Hybrid option 41

C L
contacting us vii LAB-BASE user library 67
converting libraries to another format 27 libraries
copying a library from the NIST Libraries list 26 adding, to NIST Libraries list 25
CRC Handbook of Data of Organic Compounds converting to another format 27
database 45 copying, from NIST libraries list 26
creating a library entry with your spectral data 24–27 creating entries in 24–27
deleting from the NIST Libraries list 26
custom
reports, example 52 searching
during batch reprocessing 37
user library 17, 23
in Qual Browser 32
Library Browser window
D about 4
deleting a library from the NIST Libraries list 26 Library Manager application 24
dialog boxes Library Search Constraints page
Search List 17 element constraints 46
Search Properties 32 elements in compound 47
mass spectral peak constraints 48
molecular weight 44
E name fragment 46
element constraints 46 Library Search Results window 73
elements in compound 47

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Index: M

library searches R
adding to processing method 40
Registry of Toxic Effects Chemical Substances database 45
creating a sequence for 55
reports
adding a report template to the processing method 52
M adding to processing method 50
Mass spectral peak constraints 48 printing
MassLab user library 67 in Qual Browser 36
Match factor threshold 18 in Sequence Setup 57
molecular weight, constraining a library search 44 reverse search, match factor threshold 18

N S
Name Fragment constraint 46 scan filter view 9
National Institute of Standards and Technology 1, 4 Search List dialog box 42
Neutral Loss option 41 spectrum files
adding to library 5
NIH-NCI Inventory File database 45
manually exporting 16
NIST Browser 4
Subtract Background window 12
NIST MS Search 4
subtracting background spectra 14
NIST/EPA Gas Phase IR database 45

P T
text file label, spectrum 22
Penalize Rare Compounds option 41
Thermo Library Manager application
printing reports
Convert Libraries Page 68
from Qual Browser 36
Manage Libraries Page 71
from Sequence Setup 58
thresholds, append to user library option 18
probability threshold 18
Toxic Substances Control Act Inventory database 45
processing methods
adding a library search 40
exporting a spectrum 19 U
Processing Setup window US Pharmacopoeia database 45
opening 37 user guides, Xcalibur v
Qual view user libraries
Identification page 38 adding 25
Library Search Constraints page 43 creating 21
Library Search Options page 40 including in a search
opening 37 in a processing method 42
Search List dialog box 42 in Qual Browser 32

Q V
Qual Browser window viewing a spectrum in Qual Browser 8
cursor actions in views 8
exporting a spectrum to Library Browser 16
grid layout 8
Library Search Spectrum icon 34
library searches in 32
Print dialog box 36
Search Properties dialog box 32
subtract background tool 12
using views interactively 8

76 Xcalibur Library Browser User Guide Thermo Scientific